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DNA Repair
Prepared by:Denana Sarajlid
Berina Alid
Dijana Sejinovid
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General errors in DNA replication are unavoidable.
DNA polymerases very occasionally insert the wrong
nucleotide, resulting in mispaired bases.
In the great majority of cases, the errors are quickly
corrected by the DNA polymerase itself.
If mispaired bases are not eliminated by the DNApolymerase, a DNA mismatch repair system is activated.
Chemical damage to DNA can be caused by external
mutagens
Various endogenous and exogenous sources can causedamage to DNA by altering its chemical structure
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According to the type of DNA lesion, one of several
alternative DNA repair pathways is used:
Base excision repair (BER)
Single-strand break repair
Nucleotide excision repair (NER)
Base mismatch repair
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Base excision repair
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Nucleotide excision repair
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Double-strand DNA breaks (DSBs) are normally rare in cells.
DSBs occur by accident, as a result of chemical attack onDNA by endogenous or externally induced ROS .
Unrepaired DSBs are highly dangerous to cells. The break
can lead to the inactivation of a critically important gene.
Two major DNA repair mechanisms can be deployed to
repair a DSB :
- Homologous recombination (HR)-mediated DNA repair
- Nonhomologous end joining (NHEJ).
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DNA damage may sometimes go undetected. For
example, cytosines that occur within the dinucleotide CG
are highly mutable as a result of inefficient DNA repair.Deamination of 5-methylcytosine, however, produces a
normal DNA base, thymine, that can sometimes go
undetected as an altered base.
DNA lesions may be identified but are not repaired beforeDNA replication (damage tolerance).
DNA lesions that block replication may be bypassed
rather than repaired, and non-classical DNA polymerases
are required to resume DNA synthesis (translesion
synthesis).
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References
T. Strachan, J. Goodship, P. Chinnery, Genetics and
Genomics in Medicine, Garland Science 2014
All figures in this presentation are taken from
Chapter 4 Principles of Genetic Variation of thementioned book.
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Regulation of Transcription in
Eukaryotes 1
Prepared by:
Ahme Osmanovid
Adnan Fojnica
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Control of the gene expression is far more complex ineukaryotes than in prokaryotes
Expression of eukaroyotic genes is regulated primary at
level of initiation of transcription
Regulation of Transcription in Eukaryotes includes :
cis-Acting Regulatory Sequences (Promoters and
Enhancers), Transcription Factor Binding
Sites,Transcriptional Regulatory Proteins, Structure andFunction of Transcriptional Activators
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Cis-Acting Regulatory sequences:
promoters, enhancers & silencers
We can distinguish three classes of elements on the basis of theirrelative locations.
1. Promoters:
a. the core promoter (binding site for the RNA polymerase II)
b. promoter-proximal cis-acting sequences ( binding site for
proteins that assist in the binding of RNA polymerase II to its
promoter)
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Enhancer sequences are regulatory
DNA sequences that, when bound
by specific proteins called
transcription factors, enhance thetranscription of an associated gene.
Enhancers can be located upstream,
downstream, or even within the
gene they control.
2. Enhancers
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3. Silencers
Silencers are cis-acting sequences
that are bound by repressors,thereby inhibiting activators andreducing transcription. Enhancersand silencers are similar topromoter-proximal regions in thatthey are organized as a series of cis-acting sequences that are bound bytrans-acting regulatory proteins.However, they are distinguishedfrom promoter-proximal elementsby being able to act at a distance,
sometimes 50
kb or more, and bybeing able to operate eitherupstream or downstream from thepromoter that they control.Enhancer and silencer elements are
intricately structured.
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Transcription Factor Binding Sites
The binding site of most transcription factors
consist of short DNA sequences, 6-10 base pairs.
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Transcriptional regulatory proteins
Most common transriptional regulatory factors are transcription
factors.
Transcription factor (sometimes called a sequence-specific DNA-
binding factor) is a protein that binds to specific DNA sequences,
thereby controlling the rate of transcription.
Mouse Transcription factor
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Structure and Function of Transcription
activators
Regulatory proteins that bind to DNA sequence and stimulates
transcription.
One region of the protein binds DNA, other part interacts with
proteins.
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https://www.youtube.com/watch?v=nLAF5i1X7DI
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References
1. Cooper, G. M., & Hausman, R. E. (2007). The Cell: A Molecular
Approach.
2. https://www.ndsu.edu/pubweb/~mcclean/plsc731/cis-
trans/cis-trans6.htm3. http://www.nature.com/scitable/definition/enhancer-163
4. http://www.nature.com/scitable/definition/promoter-259
5. https://www.youtube.com/watch?v=nLAF5i1X7DI
6. http://www.ncbi.nlm.nih.gov/books/NBK21780/
7. http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?i
t=swf::535::535::/sites/dl/free/0072437316/120080/bio28.swf
::Transcription%20Complex%20and%20Enhancers
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Regulation of transcription in eukaryotes
2
Prepared by:
Ilderina Jusufovid
Layla Abdelilah
Selma Demirovid
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1.Eukaryotic Repressors
Repressor is any protein that binds to DNA and thusregulates the expression of genes by decreasing therate of transcription.
Gene expression in eukaryotic cells is regulated byrepressors as well as by transcriptional activators.
In some cases, eukaryotic repressors simply interferewith the binding of other transcription factors toDNA.
Other repressors compete with activators for bindingto specific regulatory sequences.
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2.Relationship of Chromatin Structure to
Transcription
Chromatin is a complex of macromolecules found in
cells,consisting of DNA,protein and RNA.
Several modifications are characteristics oftranscriptionally active chromatin:modifications of
histones,rearrangements of nucleosomes, and the
association of two ninhistone chromosomal proteins
called:HMGN proteins with the nucleosomes with
actively transribed genes.
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Histone Acetylation neutralizes (+) charges on amino-
terminal tails that are rich in lysine residues andprevents binding to adjacent nucleosome which resultsloose chromatin structure, allowing for increasedtranscription.
Methylation of lysine and arginine residues promotes
repression and chromatin condensation. Phosphorylation of serine residues can prevent
condensation, if phosphorylation is adjacent to methylgroup.
Combinations of histone modifications constitute ahistone coe.
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3.Regulation of transcription by non-coding
RNA-s
RNA interference- is a biological process in whichRNA molecules inhibit gene expression, typically by
causing the destruction of specific mRNA molecule.
Micro RNA + RISC = destroying mRNA
Micro RNA + RITS = heterochromatin
X chromosome inactivation- Xist
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4.Methylation
Cytosine residues in
vertebrate DNA can be
modified by the addition of
methyl groups at the 5-carbon position .
DNA is methylated
specifically at the C's that
precede G's in the DNAchain (CpG dinucleotides).
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References
http://themedicalbiochemistrypage.org/gene-regulation.php
http://genesdev.cshlp.org/content/21/1/11.full
http://www.bloodjournal.org/content/93/12/4059?sso-
checked=true
http://www.ncbi.nlm.nih.gov/books/NBK9904/
http://www.news-medical.net/health/What-is-DNA-
Methylation.aspx
Cooper, G., & Hausman, R. (2007). The cell: A molecularapproach (4th ed.). Washington, D.C.: ASM Press
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RNA PROCESSING
Prepared by:
Belma Alispahid
Leila Kekid
Jasin Hoid
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PROCESSING OF rRNAs
Eukaryotic cells 4 rRNAs 5S rRNA from a separate gene
18S, 28S and 5.8S from a common pre-rRNA
Final products 18 S, 5.8S H-bonded to 28S
rRNA processing cleavages + addition of methyl groups
to the bases and sugar moieties of specific nucleotides(function unknown).
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PROCESSING OF tRNAs
Derived from pre-tRNAs
Cleavage at 5 by RNAse Pribozyme
Cleavage at 3 by conventionalprotein RNAse
CCA terminus ae to 3 en
Bases modified (10%):
Uridines modifications:ribothymidine (T)
dihydrouridine (DHU)pseudouridine ()
Guanosines modifications:inosine (I)
methylguanosine (mG)
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PROCESSING OF mRNA
5 terminus cappingwith 7-
methylguanosine
(m7G)
Placing of GTP in
reverse orientation
Methylation of G
residues
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3 Polyadenylation
Polyadenylation signals ; hexanucleotide AAUAAA
Endonuclease cleaves the pre-mRNA CA sequence Poly-A polymerase as As on 3 en
regulate both translation and mRNA stability
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SPLICING MECHANISMS
In vitro splicing
bacteriophage RNA
polymerases
transcription nuclear
extract 2 steps
3 critical sequence
element
snRNAs and snRNPs
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Capability of self-splicing
Revealed self-splicing RNAs in protozoan, mitochondria,
chloroplasts, and bacteria Divided into two classes on the basis of their reaction
mechanisms:
Group I introns
Group II introns
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ALTERNATIVE SPLICING
Alternative splicing-different mRNAs from differentcombinations of 5and 3 splice sites.
Transcriptional regulatory protein ;
Activator VS Repressor
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RNA EDITING
RNA editing refers to RNA processing that alter the protein-
coding sequences of some mRNAs:
deamination of cytosine to uridine
adenosine to inosine
Editing of apolipoprotein B mRNA
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RNA DEGRADATION
rRNAs and tRNAs are very stable (90% in cells) mRNA degradation: shortening of poly-A tails removal of 5
cap degradation of the RNA by nucleases acting from both
ends (mammalian mRNA half-life: 30min-20h)
mRNA stability: Unstable mRNAs: regulatory proteins, transcription factors
Stable mRNAs: in response to extracellular signals
(transferrin mRNA)
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SOURCES
http://www.ncbi.nlm.nih.gov/books/NBK9864/
http://www.ncbi.nlm.nih.gov/books/NBK21563/
http://www.csun.edu/~cmalone/pdf360/Ch13-
2RNAprocess.pdf
http://study.com/academy/lesson/rna-splicing-of-introns-
exons-and-other-forms-of-rna-processing.html
https://www.youtube.com/watch?v=MblGu1okRuY
https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-
eukaryotes-109/
http://www.ncbi.nlm.nih.gov/books/NBK9864/http://www.ncbi.nlm.nih.gov/books/NBK21563/http://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttps://www.youtube.com/watch?v=MblGu1okRuYhttps://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.youtube.com/watch?v=MblGu1okRuYhttps://www.youtube.com/watch?v=MblGu1okRuYhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-form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